John Cridland, who has chaired Transport for the North (TfN) since 2015, accepted an offer from Cabinet Minister Grant Shapps to be president of the new Northern Transport Acceleration Council.
The council, which the Government says will offer northern leaders a direct line to Ministers and get major projects delivered more quickly, had its first 'virtual' meeting this week.
And the presence of Mr Cridland, a former Director-General of the Confederation of British Industry, as its president will cast further doubt on the future of TfN.
Transport Secretary Grant Shapps described the strategic body - which is reliant on government funding and lacks tax-raising powers - as being "by definition a talking shop". The Yorkshire Post understands Ministers are unhappy at the lack of progress being made on major schemes like Northern Powerhouse Rail.
As President, which is an unpaid role, Mr Cridland will be responsible for "facilitating discussions, setting out key issues in meetings to be considered on behalf of members, and providing advice to members, enabling the council to function effectively to deliver on its ambition to accelerate progress in the North".
In a message to TfN colleagues, he said the new body had been set up to "find ways to speed up transport improvements".
He said: "The Secretary of State has asked me to become President of the council and after consideration I have accepted this invitation, in order to provide an important link to TfN and in order to sustain Transport for the North's mission.
"As such I see the role as complementary to my chairmanship of Transport for the North. I can touch on this at our board meeting next week and I hope this has your support."
One source told The Yorkshire Post: “There are genuine concerns over a conflict of interest and whether John is working for politicians who represent people who live in the North or his new boss the Transport Secretary.
"There is also a worry as to how John Cridland can realistically give the same amount of time to all these paid jobs he is taking on and to what level.
"He has been at TfN since 2015 and was originally only meant to be there for 4 years and hasn’t much to show for it.”
It is understood the first physical meeting of the acceleration council will take place in the coming weeks.
The first virtual meeting, which took place on Wednesday afternoon, was interrupted when Mr Shapps had to go and vote in the Commons.
One northern leader on the call told The Yorkshire Post that the "elephant in room" was how the new body would fit in with Transport for the North, which Ministers said would "transform transport across the North of England" when it was given statutory powers in 2017.
A Department for Transport spokesman said: “We are determined to build back better at pace, and the Northern Transport Acceleration Council will provide northern leaders with a direct line to government, accelerating key decision making and delivering the vital projects communities are crying out for.
“John Cridland as President will play a central role in ensuring the Council functions effectively, supporting the Secretary of State in his role as Northern Powerhouse Minister.”
Barry White, Chief Executive at Transport for the North, said: “We want to see the delivery of transport schemes accelerated, so it’s positive to see Government putting political heft behind that agenda.
“We see the Northern Transport Acceleration Council as being complementary to the role of Transport for the North, with our current focus on strategic planning and ensuring there’s a sustained, long-term pipeline of infrastructure projects that will deliver growth for the North.”